null Mon 24 Dec 00:43:09 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2go7-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2go7-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2go7-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.2-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.2-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:43:13 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.2-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 869 and 0 Target number of residues in the AU: 869 Target solvent content: 0.6166 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 828 Adjusted target solvent content: 0.63 Input MTZ file: 2go7-3.2-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 169 Cell parameters: 155.000 155.000 88.440 90.000 90.000 120.000 Input sequence file: 2go7-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6624 target number of atoms Had to go as low as 1.10 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 134.234 3.200 Wilson plot Bfac: 59.74 20113 reflections ( 99.84 % complete ) and 0 restraints for refining 7311 atoms. Observations/parameters ratio is 0.69 ------------------------------------------------------ Starting model: R = 0.3341 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2638 (Rfree = 0.000) for 7311 atoms. Found 65 (65 requested) and removed 52 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 2.60 Search for helices and strands: 0 residues in 0 chains, 7480 seeds are put forward NCS extension: 0 residues added, 7480 seeds are put forward Round 1: 524 peptides, 81 chains. Longest chain 18 peptides. Score 0.455 Round 2: 592 peptides, 74 chains. Longest chain 26 peptides. Score 0.568 Round 3: 626 peptides, 64 chains. Longest chain 36 peptides. Score 0.646 Round 4: 631 peptides, 62 chains. Longest chain 29 peptides. Score 0.658 Round 5: 617 peptides, 60 chains. Longest chain 35 peptides. Score 0.654 Taking the results from Round 4 Chains 66, Residues 569, Estimated correctness of the model 55.7 % 8 chains (155 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 10909 restraints for refining 6046 atoms. 8090 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2678 (Rfree = 0.000) for 6046 atoms. Found 54 (54 requested) and removed 58 (27 requested) atoms. Cycle 2: After refmac, R = 0.2501 (Rfree = 0.000) for 5957 atoms. Found 41 (54 requested) and removed 38 (27 requested) atoms. Cycle 3: After refmac, R = 0.2415 (Rfree = 0.000) for 5911 atoms. Found 37 (53 requested) and removed 40 (26 requested) atoms. Cycle 4: After refmac, R = 0.2381 (Rfree = 0.000) for 5871 atoms. Found 32 (53 requested) and removed 32 (26 requested) atoms. Cycle 5: After refmac, R = 0.2336 (Rfree = 0.000) for 5856 atoms. Found 27 (52 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.07 2.57 Search for helices and strands: 0 residues in 0 chains, 6096 seeds are put forward NCS extension: 19 residues added (23 deleted due to clashes), 6115 seeds are put forward Round 1: 596 peptides, 70 chains. Longest chain 24 peptides. Score 0.591 Round 2: 655 peptides, 63 chains. Longest chain 38 peptides. Score 0.675 Round 3: 638 peptides, 61 chains. Longest chain 42 peptides. Score 0.669 Round 4: 636 peptides, 60 chains. Longest chain 27 peptides. Score 0.671 Round 5: 623 peptides, 62 chains. Longest chain 27 peptides. Score 0.651 Taking the results from Round 2 Chains 68, Residues 592, Estimated correctness of the model 59.7 % 6 chains (128 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 11274 restraints for refining 6048 atoms. 8428 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2576 (Rfree = 0.000) for 6048 atoms. Found 54 (54 requested) and removed 52 (27 requested) atoms. Cycle 7: After refmac, R = 0.2388 (Rfree = 0.000) for 6019 atoms. Found 34 (54 requested) and removed 42 (27 requested) atoms. Cycle 8: After refmac, R = 0.2336 (Rfree = 0.000) for 5978 atoms. Found 33 (53 requested) and removed 33 (26 requested) atoms. Cycle 9: After refmac, R = 0.2282 (Rfree = 0.000) for 5970 atoms. Found 9 (53 requested) and removed 27 (26 requested) atoms. Cycle 10: After refmac, R = 0.2248 (Rfree = 0.000) for 5939 atoms. Found 14 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 2.58 Search for helices and strands: 0 residues in 0 chains, 6157 seeds are put forward NCS extension: 22 residues added (14 deleted due to clashes), 6179 seeds are put forward Round 1: 605 peptides, 67 chains. Longest chain 24 peptides. Score 0.613 Round 2: 650 peptides, 58 chains. Longest chain 39 peptides. Score 0.690 Round 3: 658 peptides, 61 chains. Longest chain 41 peptides. Score 0.685 Round 4: 638 peptides, 61 chains. Longest chain 41 peptides. Score 0.669 Round 5: 622 peptides, 61 chains. Longest chain 32 peptides. Score 0.655 Taking the results from Round 2 Chains 61, Residues 592, Estimated correctness of the model 63.0 % 9 chains (149 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 11257 restraints for refining 6048 atoms. 8343 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2528 (Rfree = 0.000) for 6048 atoms. Found 54 (54 requested) and removed 78 (27 requested) atoms. Cycle 12: After refmac, R = 0.2386 (Rfree = 0.000) for 5998 atoms. Found 43 (54 requested) and removed 39 (27 requested) atoms. Cycle 13: After refmac, R = 0.2361 (Rfree = 0.000) for 5978 atoms. Found 32 (53 requested) and removed 31 (26 requested) atoms. Cycle 14: After refmac, R = 0.2291 (Rfree = 0.000) for 5958 atoms. Found 12 (53 requested) and removed 28 (26 requested) atoms. Cycle 15: After refmac, R = 0.2235 (Rfree = 0.000) for 5929 atoms. Found 22 (53 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 2.58 Search for helices and strands: 0 residues in 0 chains, 6131 seeds are put forward NCS extension: 22 residues added (29 deleted due to clashes), 6153 seeds are put forward Round 1: 604 peptides, 64 chains. Longest chain 29 peptides. Score 0.625 Round 2: 646 peptides, 57 chains. Longest chain 26 peptides. Score 0.691 Round 3: 644 peptides, 61 chains. Longest chain 37 peptides. Score 0.674 Round 4: 634 peptides, 58 chains. Longest chain 46 peptides. Score 0.677 Round 5: 627 peptides, 58 chains. Longest chain 35 peptides. Score 0.671 Taking the results from Round 2 Chains 64, Residues 589, Estimated correctness of the model 63.2 % 10 chains (156 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 10945 restraints for refining 6047 atoms. 8022 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2439 (Rfree = 0.000) for 6047 atoms. Found 54 (54 requested) and removed 47 (27 requested) atoms. Cycle 17: After refmac, R = 0.2313 (Rfree = 0.000) for 6039 atoms. Found 22 (54 requested) and removed 35 (27 requested) atoms. Cycle 18: After refmac, R = 0.2257 (Rfree = 0.000) for 6008 atoms. Found 21 (54 requested) and removed 29 (27 requested) atoms. Cycle 19: After refmac, R = 0.2198 (Rfree = 0.000) for 5994 atoms. Found 17 (53 requested) and removed 26 (26 requested) atoms. Cycle 20: After refmac, R = 0.2175 (Rfree = 0.000) for 5977 atoms. Found 16 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 2.59 Search for helices and strands: 0 residues in 0 chains, 6193 seeds are put forward NCS extension: 12 residues added (14 deleted due to clashes), 6205 seeds are put forward Round 1: 604 peptides, 72 chains. Longest chain 21 peptides. Score 0.589 Round 2: 630 peptides, 59 chains. Longest chain 26 peptides. Score 0.670 Round 3: 617 peptides, 58 chains. Longest chain 48 peptides. Score 0.663 Round 4: 622 peptides, 61 chains. Longest chain 30 peptides. Score 0.655 Round 5: 620 peptides, 62 chains. Longest chain 24 peptides. Score 0.649 Taking the results from Round 2 Chains 63, Residues 571, Estimated correctness of the model 58.5 % 6 chains (98 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 11705 restraints for refining 6046 atoms. 9078 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2474 (Rfree = 0.000) for 6046 atoms. Found 54 (54 requested) and removed 38 (27 requested) atoms. Cycle 22: After refmac, R = 0.2240 (Rfree = 0.000) for 6042 atoms. Found 32 (54 requested) and removed 35 (27 requested) atoms. Cycle 23: After refmac, R = 0.2140 (Rfree = 0.000) for 6027 atoms. Found 19 (54 requested) and removed 28 (27 requested) atoms. Cycle 24: After refmac, R = 0.2086 (Rfree = 0.000) for 6009 atoms. Found 12 (54 requested) and removed 28 (27 requested) atoms. Cycle 25: After refmac, R = 0.2058 (Rfree = 0.000) for 5989 atoms. Found 10 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.61 Search for helices and strands: 0 residues in 0 chains, 6209 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 6227 seeds are put forward Round 1: 596 peptides, 71 chains. Longest chain 31 peptides. Score 0.586 Round 2: 602 peptides, 58 chains. Longest chain 27 peptides. Score 0.650 Round 3: 610 peptides, 58 chains. Longest chain 31 peptides. Score 0.657 Round 4: 605 peptides, 65 chains. Longest chain 27 peptides. Score 0.622 Round 5: 605 peptides, 61 chains. Longest chain 36 peptides. Score 0.639 Taking the results from Round 3 Chains 60, Residues 552, Estimated correctness of the model 55.5 % 4 chains (87 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 11914 restraints for refining 6047 atoms. 9386 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2385 (Rfree = 0.000) for 6047 atoms. Found 53 (54 requested) and removed 46 (27 requested) atoms. Cycle 27: After refmac, R = 0.2211 (Rfree = 0.000) for 6029 atoms. Found 22 (54 requested) and removed 32 (27 requested) atoms. Cycle 28: After refmac, R = 0.2120 (Rfree = 0.000) for 6003 atoms. Found 7 (54 requested) and removed 39 (27 requested) atoms. Cycle 29: After refmac, R = 0.2072 (Rfree = 0.000) for 5963 atoms. Found 12 (53 requested) and removed 26 (26 requested) atoms. Cycle 30: After refmac, R = 0.2037 (Rfree = 0.000) for 5943 atoms. Found 12 (53 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.11 2.60 Search for helices and strands: 0 residues in 0 chains, 6149 seeds are put forward NCS extension: 10 residues added (14 deleted due to clashes), 6159 seeds are put forward Round 1: 579 peptides, 70 chains. Longest chain 29 peptides. Score 0.573 Round 2: 622 peptides, 56 chains. Longest chain 32 peptides. Score 0.675 Round 3: 598 peptides, 60 chains. Longest chain 24 peptides. Score 0.637 Round 4: 609 peptides, 60 chains. Longest chain 29 peptides. Score 0.647 Round 5: 588 peptides, 61 chains. Longest chain 31 peptides. Score 0.624 Taking the results from Round 2 Chains 56, Residues 566, Estimated correctness of the model 59.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 12696 restraints for refining 6041 atoms. 10488 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2280 (Rfree = 0.000) for 6041 atoms. Found 52 (54 requested) and removed 30 (27 requested) atoms. Cycle 32: After refmac, R = 0.2140 (Rfree = 0.000) for 6055 atoms. Found 20 (54 requested) and removed 27 (27 requested) atoms. Cycle 33: After refmac, R = 0.2080 (Rfree = 0.000) for 6039 atoms. Found 10 (54 requested) and removed 29 (27 requested) atoms. Cycle 34: After refmac, R = 0.2035 (Rfree = 0.000) for 6016 atoms. Found 11 (54 requested) and removed 27 (27 requested) atoms. Cycle 35: After refmac, R = 0.2019 (Rfree = 0.000) for 5995 atoms. Found 14 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 2.58 Search for helices and strands: 0 residues in 0 chains, 6212 seeds are put forward NCS extension: 13 residues added (19 deleted due to clashes), 6225 seeds are put forward Round 1: 560 peptides, 68 chains. Longest chain 19 peptides. Score 0.563 Round 2: 609 peptides, 61 chains. Longest chain 42 peptides. Score 0.643 Round 3: 627 peptides, 62 chains. Longest chain 50 peptides. Score 0.655 Round 4: 609 peptides, 62 chains. Longest chain 29 peptides. Score 0.639 Round 5: 590 peptides, 64 chains. Longest chain 28 peptides. Score 0.612 Taking the results from Round 3 Chains 66, Residues 565, Estimated correctness of the model 55.0 % 8 chains (174 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 10840 restraints for refining 6048 atoms. 7924 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2452 (Rfree = 0.000) for 6048 atoms. Found 50 (54 requested) and removed 52 (27 requested) atoms. Cycle 37: After refmac, R = 0.2299 (Rfree = 0.000) for 6012 atoms. Found 26 (54 requested) and removed 33 (27 requested) atoms. Cycle 38: After refmac, R = 0.2230 (Rfree = 0.000) for 5983 atoms. Found 21 (53 requested) and removed 29 (26 requested) atoms. Cycle 39: After refmac, R = 0.2190 (Rfree = 0.000) for 5968 atoms. Found 16 (53 requested) and removed 27 (26 requested) atoms. Cycle 40: After refmac, R = 0.2164 (Rfree = 0.000) for 5950 atoms. Found 14 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 2.60 Search for helices and strands: 0 residues in 0 chains, 6164 seeds are put forward NCS extension: 38 residues added (32 deleted due to clashes), 6202 seeds are put forward Round 1: 574 peptides, 67 chains. Longest chain 27 peptides. Score 0.582 Round 2: 593 peptides, 62 chains. Longest chain 32 peptides. Score 0.624 Round 3: 599 peptides, 63 chains. Longest chain 31 peptides. Score 0.625 Round 4: 603 peptides, 63 chains. Longest chain 27 peptides. Score 0.629 Round 5: 585 peptides, 60 chains. Longest chain 27 peptides. Score 0.625 Taking the results from Round 4 Chains 67, Residues 540, Estimated correctness of the model 48.6 % 6 chains (83 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 11940 restraints for refining 6048 atoms. 9504 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2444 (Rfree = 0.000) for 6048 atoms. Found 54 (54 requested) and removed 49 (27 requested) atoms. Cycle 42: After refmac, R = 0.2288 (Rfree = 0.000) for 6044 atoms. Found 21 (54 requested) and removed 34 (27 requested) atoms. Cycle 43: After refmac, R = 0.2202 (Rfree = 0.000) for 6011 atoms. Found 15 (54 requested) and removed 30 (27 requested) atoms. Cycle 44: After refmac, R = 0.2153 (Rfree = 0.000) for 5990 atoms. Found 13 (53 requested) and removed 28 (26 requested) atoms. Cycle 45: After refmac, R = 0.2141 (Rfree = 0.000) for 5964 atoms. Found 11 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 2.62 Search for helices and strands: 0 residues in 0 chains, 6169 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 6189 seeds are put forward Round 1: 514 peptides, 71 chains. Longest chain 31 peptides. Score 0.496 Round 2: 572 peptides, 60 chains. Longest chain 28 peptides. Score 0.613 Round 3: 562 peptides, 63 chains. Longest chain 22 peptides. Score 0.589 Round 4: 556 peptides, 57 chains. Longest chain 27 peptides. Score 0.611 Round 5: 546 peptides, 63 chains. Longest chain 27 peptides. Score 0.572 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 62, Residues 512, Estimated correctness of the model 44.5 % 3 chains (53 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2go7-3_warpNtrace.pdb as input Building loops using Loopy2018 62 chains (512 residues) following loop building 3 chains (53 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20113 reflections ( 99.84 % complete ) and 12492 restraints for refining 6048 atoms. 10298 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2386 (Rfree = 0.000) for 6048 atoms. Found 0 (54 requested) and removed 21 (27 requested) atoms. Cycle 47: After refmac, R = 0.2280 (Rfree = 0.000) for 6014 atoms. Found 0 (54 requested) and removed 1 (27 requested) atoms. Cycle 48: After refmac, R = 0.2251 (Rfree = 0.000) for 6005 atoms. Found 0 (53 requested) and removed 3 (26 requested) atoms. Cycle 49: After refmac, R = 0.2218 (Rfree = 0.000) for 5998 atoms. Found 0 (53 requested) and removed 9 (26 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:53:03 GMT 2018 Job finished. TimeTaking 69.92 Used memory is bytes: 17203936